Starting phenix.real_space_refine
on Tue Jul 29 12:42:18 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/6zgk_11209/07_2025/6zgk_11209.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zgk_11209/07_2025/6zgk_11209.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zgk_11209/07_2025/6zgk_11209.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zgk_11209/07_2025/6zgk_11209.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zgk_11209/07_2025/6zgk_11209.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zgk_11209/07_2025/6zgk_11209.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    7710      2.51       5
     N    1875      2.21       5
     O    2025      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11630
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2326
          Classifications: {'peptide': 307}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 288}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 170
          Unresolved non-hydrogen angles: 218
          Unresolved non-hydrogen dihedrals: 136
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 127
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 4.88, per 1000 atoms: 0.42
  Number of scatterers: 11630
  At special positions: 0
  Unit cell: (92.66, 91.02, 115.62, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      20     16.00
     O    2025      8.00
     N    1875      7.00
     C    7710      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.30
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3010

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      34.2% alpha, 25.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 196 through 201
    Processing helix  chain 'A' and resid 201 through 214
      removed outlier: 3.744A  pdb=" N   MET A 205 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A 209 " --> pdb=" O   MET A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 243
      removed outlier: 4.027A  pdb=" N   THR A 226 " --> pdb=" O   GLU A 222 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR A 231 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 282
      removed outlier: 3.674A  pdb=" N   PHE A 260 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 315
      removed outlier: 3.984A  pdb=" N   ILE A 297 " --> pdb=" O   ARG A 293 " (cutoff:3.500A)
      Proline residue:  A 300  - end of helix
    Processing helix  chain 'B' and resid 196 through 201
    Processing helix  chain 'B' and resid 201 through 214
      removed outlier: 3.744A  pdb=" N   MET B 205 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU B 209 " --> pdb=" O   MET B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 243
      removed outlier: 4.027A  pdb=" N   THR B 226 " --> pdb=" O   GLU B 222 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR B 231 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 282
      removed outlier: 3.673A  pdb=" N   PHE B 260 " --> pdb=" O   GLY B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 315
      removed outlier: 3.985A  pdb=" N   ILE B 297 " --> pdb=" O   ARG B 293 " (cutoff:3.500A)
      Proline residue:  B 300  - end of helix
    Processing helix  chain 'C' and resid 196 through 201
    Processing helix  chain 'C' and resid 201 through 214
      removed outlier: 3.744A  pdb=" N   MET C 205 " --> pdb=" O   ILE C 201 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU C 209 " --> pdb=" O   MET C 205 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 243
      removed outlier: 4.027A  pdb=" N   THR C 226 " --> pdb=" O   GLU C 222 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR C 231 " --> pdb=" O   LEU C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 254 through 282
      removed outlier: 3.673A  pdb=" N   PHE C 260 " --> pdb=" O   GLY C 256 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 315
      removed outlier: 3.985A  pdb=" N   ILE C 297 " --> pdb=" O   ARG C 293 " (cutoff:3.500A)
      Proline residue:  C 300  - end of helix
    Processing helix  chain 'D' and resid 196 through 201
    Processing helix  chain 'D' and resid 201 through 214
      removed outlier: 3.744A  pdb=" N   MET D 205 " --> pdb=" O   ILE D 201 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU D 209 " --> pdb=" O   MET D 205 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 243
      removed outlier: 4.028A  pdb=" N   THR D 226 " --> pdb=" O   GLU D 222 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR D 231 " --> pdb=" O   LEU D 227 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 254 through 282
      removed outlier: 3.673A  pdb=" N   PHE D 260 " --> pdb=" O   GLY D 256 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 284 through 315
      removed outlier: 3.985A  pdb=" N   ILE D 297 " --> pdb=" O   ARG D 293 " (cutoff:3.500A)
      Proline residue:  D 300  - end of helix
    Processing helix  chain 'E' and resid 196 through 201
    Processing helix  chain 'E' and resid 201 through 214
      removed outlier: 3.743A  pdb=" N   MET E 205 " --> pdb=" O   ILE E 201 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU E 209 " --> pdb=" O   MET E 205 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 220 through 243
      removed outlier: 4.028A  pdb=" N   THR E 226 " --> pdb=" O   GLU E 222 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   THR E 231 " --> pdb=" O   LEU E 227 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 254 through 282
      removed outlier: 3.673A  pdb=" N   PHE E 260 " --> pdb=" O   GLY E 256 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 284 through 315
      removed outlier: 3.984A  pdb=" N   ILE E 297 " --> pdb=" O   ARG E 293 " (cutoff:3.500A)
      Proline residue:  E 300  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 95
      removed outlier: 4.900A  pdb=" N   ALA A  87 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   SER A 107 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL A  89 " --> pdb=" O   ARG A 105 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ARG A 105 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   THR A  36 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   LEU A  30 " --> pdb=" O   THR A  36 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LYS A  38 " --> pdb=" O   TYR A  28 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   PHE A  42 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   LEU A  24 " --> pdb=" O   PHE A  42 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   SER A  44 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   ILE A  22 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   SER A  46 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   THR A  20 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   LYS A  48 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   VAL A  18 " --> pdb=" O   LYS A  48 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   LEU A  16 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ALA A 143 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL A  18 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78
      removed outlier: 6.685A  pdb=" N   ASP A 185 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA A 167 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLN A 187 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE A 165 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ARG A 189 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 86 through 95
      removed outlier: 4.900A  pdb=" N   ALA B  87 " --> pdb=" O   SER B 107 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   SER B 107 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL B  89 " --> pdb=" O   ARG B 105 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ARG B 105 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   THR B  36 " --> pdb=" O   LEU B  30 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   LEU B  30 " --> pdb=" O   THR B  36 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   LYS B  38 " --> pdb=" O   TYR B  28 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   PHE B  42 " --> pdb=" O   LEU B  24 " (cutoff:3.500A)
      removed outlier: 5.705A  pdb=" N   LEU B  24 " --> pdb=" O   PHE B  42 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   SER B  44 " --> pdb=" O   ILE B  22 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   ILE B  22 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   SER B  46 " --> pdb=" O   THR B  20 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   THR B  20 " --> pdb=" O   SER B  46 " (cutoff:3.500A)
      removed outlier: 8.306A  pdb=" N   LYS B  48 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   VAL B  18 " --> pdb=" O   LYS B  48 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   LEU B  16 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ALA B 143 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL B  18 " --> pdb=" O   ALA B 143 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 78
      removed outlier: 6.686A  pdb=" N   ASP B 185 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA B 167 " --> pdb=" O   ASP B 185 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN B 187 " --> pdb=" O   PHE B 165 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   PHE B 165 " --> pdb=" O   GLN B 187 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ARG B 189 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 86 through 95
      removed outlier: 4.899A  pdb=" N   ALA C  87 " --> pdb=" O   SER C 107 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER C 107 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL C  89 " --> pdb=" O   ARG C 105 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ARG C 105 " --> pdb=" O   VAL C  89 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   THR C  36 " --> pdb=" O   LEU C  30 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   LEU C  30 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LYS C  38 " --> pdb=" O   TYR C  28 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   PHE C  42 " --> pdb=" O   LEU C  24 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   LEU C  24 " --> pdb=" O   PHE C  42 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   SER C  44 " --> pdb=" O   ILE C  22 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   ILE C  22 " --> pdb=" O   SER C  44 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   SER C  46 " --> pdb=" O   THR C  20 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   THR C  20 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      removed outlier: 8.306A  pdb=" N   LYS C  48 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   VAL C  18 " --> pdb=" O   LYS C  48 " (cutoff:3.500A)
      removed outlier: 6.076A  pdb=" N   LEU C  16 " --> pdb=" O   VAL C 141 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ALA C 143 " --> pdb=" O   LEU C  16 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL C  18 " --> pdb=" O   ALA C 143 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 78
      removed outlier: 6.685A  pdb=" N   ASP C 185 " --> pdb=" O   ALA C 167 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ALA C 167 " --> pdb=" O   ASP C 185 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   GLN C 187 " --> pdb=" O   PHE C 165 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   PHE C 165 " --> pdb=" O   GLN C 187 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ARG C 189 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 86 through 95
      removed outlier: 4.899A  pdb=" N   ALA D  87 " --> pdb=" O   SER D 107 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER D 107 " --> pdb=" O   ALA D  87 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL D  89 " --> pdb=" O   ARG D 105 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ARG D 105 " --> pdb=" O   VAL D  89 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   THR D  36 " --> pdb=" O   LEU D  30 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   LEU D  30 " --> pdb=" O   THR D  36 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LYS D  38 " --> pdb=" O   TYR D  28 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   PHE D  42 " --> pdb=" O   LEU D  24 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   LEU D  24 " --> pdb=" O   PHE D  42 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   SER D  44 " --> pdb=" O   ILE D  22 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   ILE D  22 " --> pdb=" O   SER D  44 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   SER D  46 " --> pdb=" O   THR D  20 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   THR D  20 " --> pdb=" O   SER D  46 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   LYS D  48 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   VAL D  18 " --> pdb=" O   LYS D  48 " (cutoff:3.500A)
      removed outlier: 6.074A  pdb=" N   LEU D  16 " --> pdb=" O   VAL D 141 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ALA D 143 " --> pdb=" O   LEU D  16 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL D  18 " --> pdb=" O   ALA D 143 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 76 through 78
      removed outlier: 6.684A  pdb=" N   ASP D 185 " --> pdb=" O   ALA D 167 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA D 167 " --> pdb=" O   ASP D 185 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLN D 187 " --> pdb=" O   PHE D 165 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE D 165 " --> pdb=" O   GLN D 187 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ARG D 189 " --> pdb=" O   GLU D 163 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 86 through 95
      removed outlier: 4.899A  pdb=" N   ALA E  87 " --> pdb=" O   SER E 107 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   SER E 107 " --> pdb=" O   ALA E  87 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   VAL E  89 " --> pdb=" O   ARG E 105 " (cutoff:3.500A)
      removed outlier: 5.783A  pdb=" N   ARG E 105 " --> pdb=" O   VAL E  89 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   THR E  36 " --> pdb=" O   LEU E  30 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   LEU E  30 " --> pdb=" O   THR E  36 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   LYS E  38 " --> pdb=" O   TYR E  28 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   PHE E  42 " --> pdb=" O   LEU E  24 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   LEU E  24 " --> pdb=" O   PHE E  42 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   SER E  44 " --> pdb=" O   ILE E  22 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   ILE E  22 " --> pdb=" O   SER E  44 " (cutoff:3.500A)
      removed outlier: 7.157A  pdb=" N   SER E  46 " --> pdb=" O   THR E  20 " (cutoff:3.500A)
      removed outlier: 5.503A  pdb=" N   THR E  20 " --> pdb=" O   SER E  46 " (cutoff:3.500A)
      removed outlier: 8.305A  pdb=" N   LYS E  48 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   VAL E  18 " --> pdb=" O   LYS E  48 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   LEU E  16 " --> pdb=" O   VAL E 141 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   ALA E 143 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL E  18 " --> pdb=" O   ALA E 143 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 76 through 78
      removed outlier: 6.685A  pdb=" N   ASP E 185 " --> pdb=" O   ALA E 167 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   ALA E 167 " --> pdb=" O   ASP E 185 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   GLN E 187 " --> pdb=" O   PHE E 165 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   PHE E 165 " --> pdb=" O   GLN E 187 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ARG E 189 " --> pdb=" O   GLU E 163 " (cutoff:3.500A)

    550 hydrogen bonds defined for protein.
    1620 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.64

  Time building geometry restraints manager: 3.88 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 3570
        1.34 -     1.46: 2515
        1.46 -     1.58: 5820
        1.58 -     1.69: 0
        1.69 -     1.81: 35
  Bond restraints: 11940
  Sorted by residual:
  bond pdb=" N   THR B 158 "
       pdb=" CA  THR B 158 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.27e-02 6.20e+03 6.02e+00
  bond pdb=" N   THR D 158 "
       pdb=" CA  THR D 158 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.27e-02 6.20e+03 5.83e+00
  bond pdb=" N   THR A 158 "
       pdb=" CA  THR A 158 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.031 1.27e-02 6.20e+03 5.81e+00
  bond pdb=" N   THR E 158 "
       pdb=" CA  THR E 158 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.27e-02 6.20e+03 5.70e+00
  bond pdb=" N   TRP A 160 "
       pdb=" CA  TRP A 160 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.29e-02 6.01e+03 5.66e+00
  ... (remaining 11935 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 15238
        1.10 -     2.19: 862
        2.19 -     3.29: 184
        3.29 -     4.39: 76
        4.39 -     5.48: 35
  Bond angle restraints: 16395
  Sorted by residual:
  angle pdb=" CA  LEU E 157 "
        pdb=" C   LEU E 157 "
        pdb=" O   LEU E 157 "
      ideal   model   delta    sigma   weight residual
     122.44  118.20    4.24 1.32e+00 5.74e-01 1.03e+01
  angle pdb=" CA  LEU B 157 "
        pdb=" C   LEU B 157 "
        pdb=" O   LEU B 157 "
      ideal   model   delta    sigma   weight residual
     122.44  118.21    4.23 1.32e+00 5.74e-01 1.03e+01
  angle pdb=" CA  LEU C 157 "
        pdb=" C   LEU C 157 "
        pdb=" O   LEU C 157 "
      ideal   model   delta    sigma   weight residual
     122.44  118.21    4.23 1.32e+00 5.74e-01 1.03e+01
  angle pdb=" CA  LEU D 157 "
        pdb=" C   LEU D 157 "
        pdb=" O   LEU D 157 "
      ideal   model   delta    sigma   weight residual
     122.44  118.23    4.21 1.32e+00 5.74e-01 1.02e+01
  angle pdb=" CA  LEU A 157 "
        pdb=" C   LEU A 157 "
        pdb=" O   LEU A 157 "
      ideal   model   delta    sigma   weight residual
     122.44  118.25    4.19 1.32e+00 5.74e-01 1.01e+01
  ... (remaining 16390 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.88: 6011
       10.88 -    21.77: 639
       21.77 -    32.65: 245
       32.65 -    43.53: 105
       43.53 -    54.42: 20
  Dihedral angle restraints: 7020
    sinusoidal: 2415
      harmonic: 4605
  Sorted by residual:
  dihedral pdb=" CA  CYS D  27 "
           pdb=" C   CYS D  27 "
           pdb=" N   TYR D  28 "
           pdb=" CA  TYR D  28 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.38  -25.62     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  CYS B  27 "
           pdb=" C   CYS B  27 "
           pdb=" N   TYR B  28 "
           pdb=" CA  TYR B  28 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.39  -25.61     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  CYS A  27 "
           pdb=" C   CYS A  27 "
           pdb=" N   TYR A  28 "
           pdb=" CA  TYR A  28 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.40  -25.60     0      5.00e+00 4.00e-02 2.62e+01
  ... (remaining 7017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1162
       0.034 -    0.068: 520
       0.068 -    0.102: 237
       0.102 -    0.135: 67
       0.135 -    0.169: 14
  Chirality restraints: 2000
  Sorted by residual:
  chirality pdb=" CA  THR B 158 "
            pdb=" N   THR B 158 "
            pdb=" C   THR B 158 "
            pdb=" CB  THR B 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.70   -0.17 2.00e-01 2.50e+01 7.16e-01
  chirality pdb=" CA  THR C 158 "
            pdb=" N   THR C 158 "
            pdb=" C   THR C 158 "
            pdb=" CB  THR C 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.69   -0.16 2.00e-01 2.50e+01 6.68e-01
  chirality pdb=" CA  THR E 158 "
            pdb=" N   THR E 158 "
            pdb=" C   THR E 158 "
            pdb=" CB  THR E 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.69   -0.16 2.00e-01 2.50e+01 6.67e-01
  ... (remaining 1997 not shown)

  Planarity restraints: 2035
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E  73 "    0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO E  74 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO E  74 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO E  74 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  73 "    0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO D  74 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO D  74 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D  74 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A  73 "    0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO A  74 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A  74 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  74 "    0.027 5.00e-02 4.00e+02
  ... (remaining 2032 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 173
        2.67 -     3.23: 11401
        3.23 -     3.78: 17409
        3.78 -     4.34: 22585
        4.34 -     4.90: 37951
  Nonbonded interactions: 89519
  Sorted by model distance:
  nonbonded pdb=" O   VAL A  90 "
            pdb=" NH1 ARG B 133 "
     model   vdw
     2.111 3.120
  nonbonded pdb=" O   VAL B  90 "
            pdb=" NH1 ARG C 133 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" O   VAL C  90 "
            pdb=" NH1 ARG D 133 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" O   VAL D  90 "
            pdb=" NH1 ARG E 133 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" NH1 ARG A 133 "
            pdb=" O   VAL E  90 "
     model   vdw
     2.212 3.120
  ... (remaining 89514 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.10
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.760
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5282
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  11940  Z= 0.266
  Angle     :  0.681   5.483  16395  Z= 0.389
  Chirality :  0.047   0.169   2000
  Planarity :  0.005   0.049   2035
  Dihedral  : 12.304  54.417   4010
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.22), residues: 1515
  helix:  0.81 (0.22), residues: 480
  sheet: -0.76 (0.27), residues: 420
  loop : -0.95 (0.26), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 160 
 HIS   0.002   0.001   HIS C 235 
 PHE   0.014   0.002   PHE C 121 
 TYR   0.012   0.002   TYR D 102 
 ARG   0.009   0.001   ARG E 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09469 (  550)
  hydrogen bonds       : angle       6.73101 ( 1620)
  covalent geometry    : bond        0.00600 (11940)
  covalent geometry    : angle       0.68145 (16395)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 1.115 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.2549
  time to fit residues: 76.9789
Evaluate side-chains
  151 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.6980
   chunk 113 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 38 optimal weight:    6.9990
   chunk 76 optimal weight:    6.9990
   chunk 60 optimal weight:   20.0000
   chunk 117 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 71 optimal weight:    0.4980
   chunk 87 optimal weight:    3.9990
   chunk 136 optimal weight:    8.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.206038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.155256 restraints weight = 12824.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.152454 restraints weight = 10986.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.155726 restraints weight = 8156.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.5224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069  11940  Z= 0.253
  Angle     :  0.825   9.576  16395  Z= 0.422
  Chirality :  0.051   0.231   2000
  Planarity :  0.007   0.081   2035
  Dihedral  :  5.221  26.648   1660
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 12.62 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.21), residues: 1515
  helix:  0.93 (0.22), residues: 510
  sheet: -0.83 (0.28), residues: 385
  loop : -1.51 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP C 160 
 HIS   0.010   0.003   HIS D 235 
 PHE   0.019   0.002   PHE A 207 
 TYR   0.017   0.002   TYR C  23 
 ARG   0.013   0.001   ARG D  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05333 (  550)
  hydrogen bonds       : angle       5.24743 ( 1620)
  covalent geometry    : bond        0.00587 (11940)
  covalent geometry    : angle       0.82531 (16395)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 185
  time to evaluate  : 1.114 
Fit side-chains
REVERT: A   23 TYR cc_start: 0.6866 (t80) cc_final: 0.6566 (t80)
REVERT: A  115 ASP cc_start: 0.7807 (p0) cc_final: 0.7368 (p0)
REVERT: A  133 ARG cc_start: 0.7346 (mtp180) cc_final: 0.7064 (mtm-85)
REVERT: B   23 TYR cc_start: 0.6941 (t80) cc_final: 0.6698 (t80)
REVERT: B  115 ASP cc_start: 0.7807 (p0) cc_final: 0.7446 (p0)
REVERT: B  185 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6494 (t0)
REVERT: B  187 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6903 (mp10)
REVERT: B  309 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7992 (mm)
REVERT: C   23 TYR cc_start: 0.6901 (t80) cc_final: 0.6672 (t80)
REVERT: C  115 ASP cc_start: 0.7759 (p0) cc_final: 0.7451 (p0)
REVERT: D   23 TYR cc_start: 0.6823 (t80) cc_final: 0.6560 (t80)
REVERT: D  115 ASP cc_start: 0.7739 (p0) cc_final: 0.7417 (p0)
REVERT: E   23 TYR cc_start: 0.6936 (t80) cc_final: 0.6682 (t80)
REVERT: E  115 ASP cc_start: 0.7770 (p0) cc_final: 0.7407 (p0)
REVERT: E  185 ASP cc_start: 0.6612 (OUTLIER) cc_final: 0.6000 (t0)
  outliers start: 41
  outliers final: 21
  residues processed: 211
  average time/residue: 0.2618
  time to fit residues: 76.2441
Evaluate side-chains
  149 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 1.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  185 ASP
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  185 ASP
Chi-restraints excluded: chain E residue  242 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 148 optimal weight:    5.9990
   chunk 69 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 87 optimal weight:    0.4980
   chunk 20 optimal weight:    0.4980
   chunk 121 optimal weight:   20.0000
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 127 HIS
D 127 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.199018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.150918 restraints weight = 12963.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.146340 restraints weight = 16436.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.148261 restraints weight = 14009.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.5768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11940  Z= 0.128
  Angle     :  0.553   5.285  16395  Z= 0.287
  Chirality :  0.043   0.149   2000
  Planarity :  0.005   0.045   2035
  Dihedral  :  4.564  29.876   1660
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.34 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.22), residues: 1515
  helix:  1.58 (0.22), residues: 510
  sheet: -0.06 (0.30), residues: 370
  loop : -1.64 (0.24), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 160 
 HIS   0.002   0.001   HIS E 277 
 PHE   0.014   0.001   PHE D  37 
 TYR   0.011   0.001   TYR D 102 
 ARG   0.006   0.000   ARG B  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03980 (  550)
  hydrogen bonds       : angle       4.73702 ( 1620)
  covalent geometry    : bond        0.00290 (11940)
  covalent geometry    : angle       0.55279 (16395)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 1.225 
Fit side-chains
REVERT: A   23 TYR cc_start: 0.6818 (t80) cc_final: 0.6478 (t80)
REVERT: A   75 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7326 (mm-30)
REVERT: A  115 ASP cc_start: 0.7765 (p0) cc_final: 0.7425 (p0)
REVERT: B   23 TYR cc_start: 0.6851 (t80) cc_final: 0.6630 (t80)
REVERT: B  115 ASP cc_start: 0.7724 (p0) cc_final: 0.7490 (p0)
REVERT: B  309 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8104 (mp)
REVERT: C   23 TYR cc_start: 0.6894 (t80) cc_final: 0.6677 (t80)
REVERT: C   75 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7013 (mm-30)
REVERT: C   77 ARG cc_start: 0.7820 (mtt-85) cc_final: 0.7272 (mtt-85)
REVERT: C  133 ARG cc_start: 0.7279 (mmm-85) cc_final: 0.6970 (tpp80)
REVERT: C  185 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6206 (t0)
REVERT: D   23 TYR cc_start: 0.6854 (t80) cc_final: 0.6563 (t80)
REVERT: D   77 ARG cc_start: 0.7816 (mtt-85) cc_final: 0.7431 (mtt-85)
REVERT: D  115 ASP cc_start: 0.7750 (p0) cc_final: 0.7492 (p0)
REVERT: D  185 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.5970 (t0)
REVERT: E   23 TYR cc_start: 0.6829 (t80) cc_final: 0.6584 (t80)
REVERT: E  115 ASP cc_start: 0.7728 (p0) cc_final: 0.7306 (p0)
REVERT: E  185 ASP cc_start: 0.6839 (t70) cc_final: 0.6188 (t0)
  outliers start: 22
  outliers final: 13
  residues processed: 156
  average time/residue: 0.2307
  time to fit residues: 52.4913
Evaluate side-chains
  143 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   43 LEU
Chi-restraints excluded: chain C residue  185 ASP
Chi-restraints excluded: chain C residue  299 PHE
Chi-restraints excluded: chain D residue  185 ASP
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain D residue  299 PHE
Chi-restraints excluded: chain E residue   43 LEU
Chi-restraints excluded: chain E residue  178 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 134 optimal weight:    6.9990
   chunk 107 optimal weight:    6.9990
   chunk 105 optimal weight:    3.9990
   chunk 118 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 7 optimal weight:    5.9990
   chunk 136 optimal weight:   20.0000
   chunk 95 optimal weight:   20.0000
   chunk 114 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    1.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 127 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.194162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.148980 restraints weight = 13003.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.140061 restraints weight = 10038.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.141920 restraints weight = 10716.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.7795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11940  Z= 0.211
  Angle     :  0.666   9.645  16395  Z= 0.346
  Chirality :  0.046   0.166   2000
  Planarity :  0.006   0.055   2035
  Dihedral  :  4.507  28.876   1660
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 17.34 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.22), residues: 1515
  helix:  1.13 (0.21), residues: 510
  sheet: -0.02 (0.30), residues: 370
  loop : -1.82 (0.24), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 160 
 HIS   0.007   0.003   HIS D 235 
 PHE   0.016   0.002   PHE C 195 
 TYR   0.015   0.002   TYR C 102 
 ARG   0.010   0.001   ARG B  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04331 (  550)
  hydrogen bonds       : angle       4.80176 ( 1620)
  covalent geometry    : bond        0.00492 (11940)
  covalent geometry    : angle       0.66586 (16395)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 175
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7109 (mm-30)
REVERT: A  126 LEU cc_start: 0.8195 (mt) cc_final: 0.7922 (mt)
REVERT: A  130 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7392 (mp)
REVERT: B  309 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8253 (mp)
REVERT: C   75 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7284 (mm-30)
REVERT: C  185 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7450 (t70)
REVERT: C  193 GLN cc_start: 0.8211 (mp10) cc_final: 0.7877 (mt0)
REVERT: D  130 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7145 (mp)
REVERT: D  185 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7304 (t70)
  outliers start: 56
  outliers final: 37
  residues processed: 215
  average time/residue: 0.2331
  time to fit residues: 75.5864
Evaluate side-chains
  182 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 140
  time to evaluate  : 1.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  185 ASP
Chi-restraints excluded: chain C residue  205 MET
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain D residue   20 THR
Chi-restraints excluded: chain D residue   89 VAL
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  185 ASP
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain E residue   20 THR
Chi-restraints excluded: chain E residue   89 VAL
Chi-restraints excluded: chain E residue   92 ILE
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  193 GLN
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain E residue  242 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 5 optimal weight:    0.0970
   chunk 129 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 3 optimal weight:    9.9990
   chunk 82 optimal weight:    0.5980
   chunk 48 optimal weight:    3.9990
   chunk 138 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 73 optimal weight:    9.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.3182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 127 HIS
E 127 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.195399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.150543 restraints weight = 12896.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.142728 restraints weight = 15488.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.146232 restraints weight = 14500.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.8157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11940  Z= 0.149
  Angle     :  0.570   8.369  16395  Z= 0.293
  Chirality :  0.043   0.145   2000
  Planarity :  0.005   0.050   2035
  Dihedral  :  4.416  30.619   1660
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 20.34 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.22), residues: 1515
  helix:  1.56 (0.22), residues: 490
  sheet:  0.03 (0.29), residues: 370
  loop : -1.74 (0.24), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 213 
 HIS   0.002   0.001   HIS A 277 
 PHE   0.013   0.002   PHE B  42 
 TYR   0.016   0.001   TYR E  23 
 ARG   0.007   0.000   ARG B  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03608 (  550)
  hydrogen bonds       : angle       4.65989 ( 1620)
  covalent geometry    : bond        0.00356 (11940)
  covalent geometry    : angle       0.56993 (16395)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 148
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 LEU cc_start: 0.8250 (mt) cc_final: 0.7986 (mt)
REVERT: A  130 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7615 (mp)
REVERT: B  309 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8236 (mt)
REVERT: C   75 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7185 (mm-30)
REVERT: C  185 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7305 (t70)
REVERT: D   75 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7066 (mm-30)
REVERT: D   77 ARG cc_start: 0.8126 (mtt-85) cc_final: 0.7646 (mtt-85)
REVERT: D  115 ASP cc_start: 0.8122 (p0) cc_final: 0.7908 (p0)
REVERT: D  130 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7315 (mp)
REVERT: E   75 GLU cc_start: 0.7533 (mm-30) cc_final: 0.6738 (mm-30)
REVERT: E   77 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7768 (mmt-90)
  outliers start: 43
  outliers final: 27
  residues processed: 175
  average time/residue: 0.2311
  time to fit residues: 61.9919
Evaluate side-chains
  167 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  193 GLN
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  185 ASP
Chi-restraints excluded: chain C residue  193 GLN
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain D residue  130 LEU
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  193 GLN
Chi-restraints excluded: chain D residue  205 MET
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain E residue  132 VAL
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  205 MET
Chi-restraints excluded: chain E residue  218 SER
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  246 LEU
Chi-restraints excluded: chain E residue  281 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 105 optimal weight:    5.9990
   chunk 38 optimal weight:    9.9990
   chunk 114 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 2 optimal weight:   10.0000
   chunk 81 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 108 optimal weight:    0.7980
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.189014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.143340 restraints weight = 13126.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.133083 restraints weight = 13816.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.135505 restraints weight = 12913.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.8814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11940  Z= 0.197
  Angle     :  0.615   7.380  16395  Z= 0.320
  Chirality :  0.045   0.138   2000
  Planarity :  0.005   0.051   2035
  Dihedral  :  4.385  28.816   1660
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 18.11 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.22), residues: 1515
  helix:  1.40 (0.21), residues: 490
  sheet: -0.46 (0.28), residues: 395
  loop : -1.61 (0.24), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 213 
 HIS   0.004   0.002   HIS B 277 
 PHE   0.013   0.002   PHE B 116 
 TYR   0.015   0.002   TYR B 102 
 ARG   0.006   0.001   ARG B  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03777 (  550)
  hydrogen bonds       : angle       4.71861 ( 1620)
  covalent geometry    : bond        0.00478 (11940)
  covalent geometry    : angle       0.61458 (16395)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 144
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7246 (p90)
REVERT: B  102 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7690 (p90)
REVERT: B  309 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8258 (mt)
REVERT: D  102 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7664 (p90)
REVERT: E   75 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7244 (mm-30)
  outliers start: 66
  outliers final: 48
  residues processed: 192
  average time/residue: 0.2607
  time to fit residues: 75.3585
Evaluate side-chains
  177 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 125
  time to evaluate  : 2.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  102 TYR
Chi-restraints excluded: chain A residue  125 THR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  226 THR
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  102 TYR
Chi-restraints excluded: chain C residue  125 THR
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  193 GLN
Chi-restraints excluded: chain C residue  226 THR
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  281 VAL
Chi-restraints excluded: chain D residue  102 TYR
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  193 GLN
Chi-restraints excluded: chain D residue  205 MET
Chi-restraints excluded: chain D residue  226 THR
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  270 VAL
Chi-restraints excluded: chain D residue  281 VAL
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue  132 VAL
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  193 GLN
Chi-restraints excluded: chain E residue  205 MET
Chi-restraints excluded: chain E residue  218 SER
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  270 VAL
Chi-restraints excluded: chain E residue  281 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 61 optimal weight:    0.0570
   chunk 72 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 118 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0970
   chunk 33 optimal weight:    6.9990
   chunk 101 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.5096

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 235 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.194658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.149987 restraints weight = 12998.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.141668 restraints weight = 17412.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.144047 restraints weight = 14338.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.8918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11940  Z= 0.108
  Angle     :  0.543   6.857  16395  Z= 0.278
  Chirality :  0.042   0.141   2000
  Planarity :  0.005   0.043   2035
  Dihedral  :  4.304  30.312   1660
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 21.46 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.22), residues: 1515
  helix:  1.84 (0.22), residues: 490
  sheet: -0.41 (0.27), residues: 395
  loop : -1.51 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 213 
 HIS   0.001   0.000   HIS D 235 
 PHE   0.011   0.001   PHE B 265 
 TYR   0.020   0.001   TYR D  23 
 ARG   0.005   0.000   ARG D  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03221 (  550)
  hydrogen bonds       : angle       4.51701 ( 1620)
  covalent geometry    : bond        0.00241 (11940)
  covalent geometry    : angle       0.54303 (16395)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 122
  time to evaluate  : 2.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7261 (ttm-80)
REVERT: B   77 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7900 (mtt-85)
REVERT: B  309 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.8198 (mt)
  outliers start: 42
  outliers final: 34
  residues processed: 152
  average time/residue: 0.3266
  time to fit residues: 78.2967
Evaluate side-chains
  147 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 112
  time to evaluate  : 3.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  193 GLN
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  193 GLN
Chi-restraints excluded: chain D residue  205 MET
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  246 LEU
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue  132 VAL
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  185 ASP
Chi-restraints excluded: chain E residue  205 MET
Chi-restraints excluded: chain E residue  218 SER
Chi-restraints excluded: chain E residue  281 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 46 optimal weight:    0.3980
   chunk 116 optimal weight:    3.9990
   chunk 95 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 76 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 121 optimal weight:    5.9990
   chunk 115 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.194132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.148181 restraints weight = 12887.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.142349 restraints weight = 14252.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.144457 restraints weight = 15277.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.9072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11940  Z= 0.118
  Angle     :  0.544   6.309  16395  Z= 0.279
  Chirality :  0.042   0.127   2000
  Planarity :  0.005   0.043   2035
  Dihedral  :  4.175  28.643   1660
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 21.89 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.22), residues: 1515
  helix:  1.93 (0.22), residues: 485
  sheet: -0.53 (0.26), residues: 420
  loop : -1.42 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 160 
 HIS   0.002   0.001   HIS A 277 
 PHE   0.011   0.001   PHE A 265 
 TYR   0.020   0.001   TYR D  23 
 ARG   0.005   0.000   ARG D  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03155 (  550)
  hydrogen bonds       : angle       4.41329 ( 1620)
  covalent geometry    : bond        0.00279 (11940)
  covalent geometry    : angle       0.54407 (16395)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 118
  time to evaluate  : 2.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7786 (mm-30)
REVERT: A  102 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7406 (p90)
REVERT: B   77 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7966 (mtt-85)
REVERT: B  102 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.7777 (p90)
REVERT: B  293 ARG cc_start: 0.7698 (mtm110) cc_final: 0.7192 (ttm-80)
REVERT: B  309 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8226 (mt)
REVERT: E   75 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7303 (mm-30)
  outliers start: 49
  outliers final: 37
  residues processed: 157
  average time/residue: 0.3461
  time to fit residues: 83.5119
Evaluate side-chains
  150 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 110
  time to evaluate  : 1.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  102 TYR
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  193 GLN
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  193 GLN
Chi-restraints excluded: chain D residue  205 MET
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  270 VAL
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue  132 VAL
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  185 ASP
Chi-restraints excluded: chain E residue  205 MET
Chi-restraints excluded: chain E residue  218 SER
Chi-restraints excluded: chain E residue  281 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 1 optimal weight:    7.9990
   chunk 149 optimal weight:    4.9990
   chunk 124 optimal weight:   20.0000
   chunk 75 optimal weight:    3.9990
   chunk 121 optimal weight:    7.9990
   chunk 45 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 98 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 144 optimal weight:    0.6980
   chunk 103 optimal weight:   10.0000
   overall best weight:    2.8786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.186369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.141482 restraints weight = 13213.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.136494 restraints weight = 20758.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.138968 restraints weight = 16239.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.9615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064  11940  Z= 0.275
  Angle     :  0.675   5.950  16395  Z= 0.356
  Chirality :  0.046   0.142   2000
  Planarity :  0.005   0.051   2035
  Dihedral  :  4.618  31.957   1660
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 22.58 %
    Favored  : 73.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.21), residues: 1515
  helix:  1.20 (0.21), residues: 485
  sheet: -0.65 (0.26), residues: 420
  loop : -1.51 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP D 213 
 HIS   0.007   0.002   HIS B 277 
 PHE   0.018   0.002   PHE E 195 
 TYR   0.019   0.002   TYR A 102 
 ARG   0.005   0.001   ARG C  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04179 (  550)
  hydrogen bonds       : angle       4.93151 ( 1620)
  covalent geometry    : bond        0.00677 (11940)
  covalent geometry    : angle       0.67503 (16395)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 152
  time to evaluate  : 2.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7793 (mm-30)
REVERT: A  293 ARG cc_start: 0.7756 (mtm110) cc_final: 0.7381 (ttm-80)
REVERT: B  102 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.7814 (p90)
REVERT: B  293 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7345 (ttm-80)
REVERT: B  309 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8325 (mt)
  outliers start: 47
  outliers final: 41
  residues processed: 189
  average time/residue: 0.3199
  time to fit residues: 91.2536
Evaluate side-chains
  179 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 136
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  270 VAL
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  102 TYR
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  193 GLN
Chi-restraints excluded: chain C residue  231 THR
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  281 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  185 ASP
Chi-restraints excluded: chain D residue  205 MET
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  270 VAL
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  185 ASP
Chi-restraints excluded: chain E residue  205 MET
Chi-restraints excluded: chain E residue  218 SER
Chi-restraints excluded: chain E residue  242 VAL
Chi-restraints excluded: chain E residue  281 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 113 optimal weight:    0.5980
   chunk 130 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 131 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 122 optimal weight:   10.0000
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.190849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.146303 restraints weight = 13048.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.139919 restraints weight = 16857.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.142282 restraints weight = 16911.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.9763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11940  Z= 0.148
  Angle     :  0.576   6.050  16395  Z= 0.297
  Chirality :  0.043   0.139   2000
  Planarity :  0.005   0.046   2035
  Dihedral  :  4.431  30.090   1660
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 24.03 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.22), residues: 1515
  helix:  1.60 (0.22), residues: 485
  sheet: -0.57 (0.26), residues: 420
  loop : -1.43 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 160 
 HIS   0.002   0.001   HIS B 277 
 PHE   0.011   0.001   PHE D  37 
 TYR   0.021   0.001   TYR D  23 
 ARG   0.008   0.000   ARG D  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03437 (  550)
  hydrogen bonds       : angle       4.64810 ( 1620)
  covalent geometry    : bond        0.00360 (11940)
  covalent geometry    : angle       0.57586 (16395)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3030 Ramachandran restraints generated.
    1515 Oldfield, 0 Emsley, 1515 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 128
  time to evaluate  : 1.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  293 ARG cc_start: 0.7741 (mtm110) cc_final: 0.7326 (ttm-80)
REVERT: B  102 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7841 (p90)
REVERT: B  309 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8262 (mt)
REVERT: D   77 ARG cc_start: 0.8074 (mtt-85) cc_final: 0.7789 (mtt-85)
  outliers start: 41
  outliers final: 35
  residues processed: 161
  average time/residue: 0.3159
  time to fit residues: 75.5404
Evaluate side-chains
  160 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 123
  time to evaluate  : 1.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  178 ASP
Chi-restraints excluded: chain A residue  193 GLN
Chi-restraints excluded: chain A residue  205 MET
Chi-restraints excluded: chain A residue  218 SER
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   39 VAL
Chi-restraints excluded: chain B residue  102 TYR
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain B residue  205 MET
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  242 VAL
Chi-restraints excluded: chain B residue  281 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain C residue   39 VAL
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain C residue  193 GLN
Chi-restraints excluded: chain C residue  242 VAL
Chi-restraints excluded: chain C residue  270 VAL
Chi-restraints excluded: chain C residue  281 VAL
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  144 VAL
Chi-restraints excluded: chain D residue  205 MET
Chi-restraints excluded: chain D residue  242 VAL
Chi-restraints excluded: chain D residue  270 VAL
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain E residue  144 VAL
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain E residue  205 MET
Chi-restraints excluded: chain E residue  218 SER
Chi-restraints excluded: chain E residue  281 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 127 optimal weight:    8.9990
   chunk 126 optimal weight:    7.9990
   chunk 71 optimal weight:    4.9990
   chunk 47 optimal weight:   10.0000
   chunk 139 optimal weight:    0.0570
   chunk 29 optimal weight:    4.9990
   chunk 142 optimal weight:    0.5980
   chunk 3 optimal weight:    7.9990
   chunk 124 optimal weight:   20.0000
   chunk 61 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   overall best weight:    3.7304

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.183657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.139672 restraints weight = 13186.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.132868 restraints weight = 16905.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.134013 restraints weight = 17124.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          1.0100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060  11940  Z= 0.328
  Angle     :  0.721   6.537  16395  Z= 0.379
  Chirality :  0.047   0.145   2000
  Planarity :  0.006   0.054   2035
  Dihedral  :  4.752  32.363   1660
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 23.52 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.21), residues: 1515
  helix:  0.99 (0.21), residues: 485
  sheet: -0.68 (0.26), residues: 420
  loop : -1.63 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP D 213 
 HIS   0.006   0.002   HIS B 277 
 PHE   0.019   0.002   PHE D 195 
 TYR   0.019   0.002   TYR B 102 
 ARG   0.007   0.001   ARG D  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04258 (  550)
  hydrogen bonds       : angle       5.11091 ( 1620)
  covalent geometry    : bond        0.00806 (11940)
  covalent geometry    : angle       0.72090 (16395)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3862.01 seconds
wall clock time: 73 minutes 51.48 seconds (4431.48 seconds total)